Job ID = 6452531 SRX = SRX016146 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:39:06 prefetch.2.10.7: 1) Downloading 'SRR034700'... 2020-06-21T07:39:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:41:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:41:37 prefetch.2.10.7: 'SRR034700' is valid 2020-06-21T07:41:37 prefetch.2.10.7: 1) 'SRR034700' was downloaded successfully Read 9492580 spots for SRR034700/SRR034700.sra Written 9492580 spots for SRR034700/SRR034700.sra 2020-06-21T07:42:12 prefetch.2.10.7: 1) Downloading 'SRR034701'... 2020-06-21T07:42:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:43:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:43:34 prefetch.2.10.7: 'SRR034701' is valid 2020-06-21T07:43:34 prefetch.2.10.7: 1) 'SRR034701' was downloaded successfully Read 13490540 spots for SRR034701/SRR034701.sra Written 13490540 spots for SRR034701/SRR034701.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:26 22983120 reads; of these: 22983120 (100.00%) were unpaired; of these: 692040 (3.01%) aligned 0 times 18497822 (80.48%) aligned exactly 1 time 3793258 (16.50%) aligned >1 times 96.99% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 11637806 / 22291080 = 0.5221 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 16:53:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:19: 1000000 INFO @ Sun, 21 Jun 2020 16:53:24: 2000000 INFO @ Sun, 21 Jun 2020 16:53:30: 3000000 INFO @ Sun, 21 Jun 2020 16:53:36: 4000000 INFO @ Sun, 21 Jun 2020 16:53:41: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 16:53:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:48: 6000000 INFO @ Sun, 21 Jun 2020 16:53:51: 1000000 INFO @ Sun, 21 Jun 2020 16:53:54: 7000000 INFO @ Sun, 21 Jun 2020 16:53:59: 2000000 INFO @ Sun, 21 Jun 2020 16:54:01: 8000000 INFO @ Sun, 21 Jun 2020 16:54:06: 3000000 INFO @ Sun, 21 Jun 2020 16:54:08: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 16:54:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:14: 4000000 INFO @ Sun, 21 Jun 2020 16:54:15: 10000000 INFO @ Sun, 21 Jun 2020 16:54:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:20: #1 total tags in treatment: 10653274 INFO @ Sun, 21 Jun 2020 16:54:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:54:20: 1000000 INFO @ Sun, 21 Jun 2020 16:54:20: #1 tags after filtering in treatment: 10653234 INFO @ Sun, 21 Jun 2020 16:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:20: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:21: 5000000 INFO @ Sun, 21 Jun 2020 16:54:21: #2 number of paired peaks: 588 WARNING @ Sun, 21 Jun 2020 16:54:21: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Sun, 21 Jun 2020 16:54:21: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:21: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:21: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:21: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:21: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 16:54:21: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 16:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.05_model.r INFO @ Sun, 21 Jun 2020 16:54:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:54:27: 2000000 INFO @ Sun, 21 Jun 2020 16:54:29: 6000000 INFO @ Sun, 21 Jun 2020 16:54:34: 3000000 INFO @ Sun, 21 Jun 2020 16:54:36: 7000000 INFO @ Sun, 21 Jun 2020 16:54:41: 4000000 INFO @ Sun, 21 Jun 2020 16:54:44: 8000000 INFO @ Sun, 21 Jun 2020 16:54:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:48: 5000000 INFO @ Sun, 21 Jun 2020 16:54:52: 9000000 INFO @ Sun, 21 Jun 2020 16:54:55: 6000000 INFO @ Sun, 21 Jun 2020 16:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.05_summits.bed INFO @ Sun, 21 Jun 2020 16:54:59: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (402 chroms): 2 millis pass2 - checking and writing primary data (5771 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:55:00: 10000000 INFO @ Sun, 21 Jun 2020 16:55:02: 7000000 INFO @ Sun, 21 Jun 2020 16:55:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:55:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:55:05: #1 total tags in treatment: 10653274 INFO @ Sun, 21 Jun 2020 16:55:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:55:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:55:05: #1 tags after filtering in treatment: 10653234 INFO @ Sun, 21 Jun 2020 16:55:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:05: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:06: #2 number of paired peaks: 588 WARNING @ Sun, 21 Jun 2020 16:55:06: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Sun, 21 Jun 2020 16:55:06: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:06: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:06: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:06: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:06: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 16:55:06: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 16:55:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.10_model.r INFO @ Sun, 21 Jun 2020 16:55:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:55:08: 8000000 INFO @ Sun, 21 Jun 2020 16:55:15: 9000000 INFO @ Sun, 21 Jun 2020 16:55:20: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:55:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:55:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:55:24: #1 total tags in treatment: 10653274 INFO @ Sun, 21 Jun 2020 16:55:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:55:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:55:25: #1 tags after filtering in treatment: 10653234 INFO @ Sun, 21 Jun 2020 16:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:25: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:26: #2 number of paired peaks: 588 WARNING @ Sun, 21 Jun 2020 16:55:26: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Sun, 21 Jun 2020 16:55:26: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:26: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:26: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:26: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:26: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 16:55:26: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 16:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.20_model.r INFO @ Sun, 21 Jun 2020 16:55:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:55:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.10_summits.bed INFO @ Sun, 21 Jun 2020 16:55:48: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (1766 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:55:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:56:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:56:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:56:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016146/SRX016146.20_summits.bed INFO @ Sun, 21 Jun 2020 16:56:05: Done! pass1 - making usageList (245 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 9 millis CompletedMACS2peakCalling